Starting phenix.real_space_refine on Fri Jul 26 10:22:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf2_9359/07_2024/6nf2_9359.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf2_9359/07_2024/6nf2_9359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf2_9359/07_2024/6nf2_9359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf2_9359/07_2024/6nf2_9359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf2_9359/07_2024/6nf2_9359.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nf2_9359/07_2024/6nf2_9359.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 171 5.16 5 C 20430 2.51 5 N 5331 2.21 5 O 6672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 32": "OE1" <-> "OE2" Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ASP 167": "OD1" <-> "OD2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 474": "OD1" <-> "OD2" Residue "A ASP 477": "OD1" <-> "OD2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 584": "OE1" <-> "OE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B ASP 659": "OD1" <-> "OD2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ARG 52": "NH1" <-> "NH2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 79": "OE1" <-> "OE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 107": "OD1" <-> "OD2" Residue "G ASP 141": "OD1" <-> "OD2" Residue "G GLU 153": "OE1" <-> "OE2" Residue "G ASP 167": "OD1" <-> "OD2" Residue "G TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 368": "OD1" <-> "OD2" Residue "G PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 474": "OD1" <-> "OD2" Residue "G ASP 477": "OD1" <-> "OD2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 16": "OE1" <-> "OE2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H ASP 58": "OD1" <-> "OD2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 75": "NH1" <-> "NH2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "I PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 584": "OE1" <-> "OE2" Residue "I GLU 648": "OE1" <-> "OE2" Residue "I ASP 659": "OD1" <-> "OD2" Residue "J GLU 6": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ASP 56": "OD1" <-> "OD2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 72": "OD1" <-> "OD2" Residue "J TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 61": "NH1" <-> "NH2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 77": "NH1" <-> "NH2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 107": "NH1" <-> "NH2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M ARG 52": "NH1" <-> "NH2" Residue "M PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 81": "OD1" <-> "OD2" Residue "M PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 98": "OE1" <-> "OE2" Residue "N PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 61": "NH1" <-> "NH2" Residue "N PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "O GLU 16": "OE1" <-> "OE2" Residue "O TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O ASP 58": "OD1" <-> "OD2" Residue "O ARG 66": "NH1" <-> "NH2" Residue "O ARG 75": "NH1" <-> "NH2" Residue "O TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 100": "NH1" <-> "NH2" Residue "O ASP 101": "OD1" <-> "OD2" Residue "P ARG 24": "NH1" <-> "NH2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 77": "NH1" <-> "NH2" Residue "P GLU 81": "OE1" <-> "OE2" Residue "P PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 107": "NH1" <-> "NH2" Residue "Q GLU 32": "OE1" <-> "OE2" Residue "Q TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 107": "OD1" <-> "OD2" Residue "Q ASP 141": "OD1" <-> "OD2" Residue "Q GLU 153": "OE1" <-> "OE2" Residue "Q ASP 167": "OD1" <-> "OD2" Residue "Q TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 368": "OD1" <-> "OD2" Residue "Q PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 474": "OD1" <-> "OD2" Residue "Q ASP 477": "OD1" <-> "OD2" Residue "R PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 584": "OE1" <-> "OE2" Residue "R GLU 648": "OE1" <-> "OE2" Residue "R ASP 659": "OD1" <-> "OD2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S ASP 56": "OD1" <-> "OD2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 72": "OD1" <-> "OD2" Residue "S TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 79": "OE1" <-> "OE2" Residue "T GLU 83": "OE1" <-> "OE2" Residue "T PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 17": "OE1" <-> "OE2" Residue "U ARG 52": "NH1" <-> "NH2" Residue "U PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 81": "OD1" <-> "OD2" Residue "U PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 98": "OE1" <-> "OE2" Residue "V PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 61": "NH1" <-> "NH2" Residue "V PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 6": "OE1" <-> "OE2" Residue "W GLU 16": "OE1" <-> "OE2" Residue "W TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 38": "NH1" <-> "NH2" Residue "W ASP 58": "OD1" <-> "OD2" Residue "W ARG 66": "NH1" <-> "NH2" Residue "W ARG 75": "NH1" <-> "NH2" Residue "W TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 100": "NH1" <-> "NH2" Residue "W ASP 101": "OD1" <-> "OD2" Residue "X ARG 24": "NH1" <-> "NH2" Residue "X ARG 54": "NH1" <-> "NH2" Residue "X ARG 61": "NH1" <-> "NH2" Residue "X PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 77": "NH1" <-> "NH2" Residue "X GLU 81": "OE1" <-> "OE2" Residue "X PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 107": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 32604 Number of models: 1 Model: "" Number of chains: 78 Chain: "A" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "C" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "D" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "E" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "F" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "G" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "H" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 951 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 115} Chain: "I" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "J" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "K" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "L" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "N" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "O" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 951 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 115} Chain: "P" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "Q" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "R" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "S" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "T" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "U" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "V" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "W" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 951 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 115} Chain: "X" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "r" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "2" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "3" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "7" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "8" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "9" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "AA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "BA" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "CA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "DA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "EA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "FA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "GA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "HA" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "IA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "JA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 17.47, per 1000 atoms: 0.54 Number of scatterers: 32604 At special positions: 0 Unit cell: (160.988, 152.402, 156.695, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 171 16.00 O 6672 8.00 N 5331 7.00 C 20430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 98 " - pdb=" SG CYS C 100A" distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.05 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.02 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 98 " - pdb=" SG CYS N 100A" distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 54 " - pdb=" SG CYS Q 74 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 119 " - pdb=" SG CYS Q 205 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 126 " - pdb=" SG CYS Q 196 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 131 " - pdb=" SG CYS Q 157 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 201 " - pdb=" SG CYS Q 433 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 218 " - pdb=" SG CYS Q 247 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 228 " - pdb=" SG CYS Q 239 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 296 " - pdb=" SG CYS Q 331 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 378 " - pdb=" SG CYS Q 445 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 385 " - pdb=" SG CYS Q 418 " distance=2.03 Simple disulfide: pdb=" SG CYS R 598 " - pdb=" SG CYS R 604 " distance=2.02 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.04 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 92 " distance=2.03 Simple disulfide: pdb=" SG CYS V 98 " - pdb=" SG CYS V 100A" distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 92 " distance=2.04 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 1 4 " - " MAN 1 5 " " MAN 1 5 " - " MAN 1 6 " " MAN f 4 " - " MAN f 5 " " MAN l 4 " - " MAN l 5 " " MAN l 5 " - " MAN l 6 " " MAN v 4 " - " MAN v 5 " " MANBA 4 " - " MANBA 5 " " MANHA 4 " - " MANHA 5 " " MANHA 5 " - " MANHA 6 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " MAN 1 7 " - " MAN 1 8 " " BMA 3 3 " - " MAN 3 4 " " BMA 6 3 " - " MAN 6 4 " " BMA 7 3 " - " MAN 7 4 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA f 3 " - " MAN f 4 " " BMA j 3 " - " MAN j 4 " " BMA l 3 " - " MAN l 4 " " MAN l 7 " - " MAN l 8 " " BMA n 3 " - " MAN n 4 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 4 " " BMA v 3 " - " MAN v 4 " " BMA z 3 " - " MAN z 4 " " BMABA 3 " - " MANBA 4 " " BMAFA 3 " - " MANFA 4 " " BMAHA 3 " - " MANHA 4 " " MANHA 7 " - " MANHA 8 " " BMAJA 3 " - " MANJA 4 " ALPHA1-6 " BMA 1 3 " - " MAN 1 7 " " MAN 1 7 " - " MAN 1 9 " " BMA 7 3 " - " MAN 7 5 " " BMA 9 3 " - " MAN 9 4 " " BMA b 3 " - " MAN b 5 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 6 " " BMA j 3 " - " MAN j 5 " " BMA l 3 " - " MAN l 7 " " MAN l 7 " - " MAN l 9 " " BMA r 3 " - " MAN r 5 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 6 " " BMA z 3 " - " MAN z 5 " " BMABA 3 " - " MANBA 6 " " BMAFA 3 " - " MANFA 5 " " BMAHA 3 " - " MANHA 7 " " MANHA 7 " - " MANHA 9 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGFA 2 " - " BMAFA 3 " " NAGGA 1 " - " NAGGA 2 " " NAGHA 1 " - " NAGHA 2 " " NAGHA 2 " - " BMAHA 3 " " NAGIA 1 " - " NAGIA 2 " " NAGIA 2 " - " BMAIA 3 " " NAGJA 1 " - " NAGJA 2 " " NAGJA 2 " - " BMAJA 3 " NAG-ASN " NAG 0 1 " - " ASN G 392 " " NAG 1 1 " - " ASN G 332 " " NAG 2 1 " - " ASN G 448 " " NAG 3 1 " - " ASN G 276 " " NAG 4 1 " - " ASN Q 88 " " NAG 5 1 " - " ASN Q 133 " " NAG 6 1 " - " ASN Q 137 " " NAG 7 1 " - " ASN Q 156 " " NAG 8 1 " - " ASN Q 160 " " NAG 9 1 " - " ASN Q 197 " " NAG A 634 " - " ASN A 355 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 611 " " NAG G 634 " - " ASN G 355 " " NAG I 701 " - " ASN I 637 " " NAG I 702 " - " ASN I 611 " " NAG Q 634 " - " ASN Q 355 " " NAG R 701 " - " ASN R 637 " " NAG R 702 " - " ASN R 611 " " NAG Y 1 " - " ASN A 88 " " NAG Z 1 " - " ASN A 133 " " NAG a 1 " - " ASN A 137 " " NAG b 1 " - " ASN A 156 " " NAG c 1 " - " ASN A 160 " " NAG d 1 " - " ASN A 197 " " NAG e 1 " - " ASN A 234 " " NAG f 1 " - " ASN A 262 " " NAG g 1 " - " ASN A 295 " " NAG h 1 " - " ASN A 301 " " NAG i 1 " - " ASN A 363 " " NAG j 1 " - " ASN A 386 " " NAG k 1 " - " ASN A 392 " " NAG l 1 " - " ASN A 332 " " NAG m 1 " - " ASN A 448 " " NAG n 1 " - " ASN A 276 " " NAG o 1 " - " ASN G 88 " " NAG p 1 " - " ASN G 133 " " NAG q 1 " - " ASN G 137 " " NAG r 1 " - " ASN G 156 " " NAG s 1 " - " ASN G 160 " " NAG t 1 " - " ASN G 197 " " NAG u 1 " - " ASN G 234 " " NAG v 1 " - " ASN G 262 " " NAG w 1 " - " ASN G 295 " " NAG x 1 " - " ASN G 301 " " NAG y 1 " - " ASN G 363 " " NAG z 1 " - " ASN G 386 " " NAGAA 1 " - " ASN Q 234 " " NAGBA 1 " - " ASN Q 262 " " NAGCA 1 " - " ASN Q 295 " " NAGDA 1 " - " ASN Q 301 " " NAGEA 1 " - " ASN Q 363 " " NAGFA 1 " - " ASN Q 386 " " NAGGA 1 " - " ASN Q 392 " " NAGHA 1 " - " ASN Q 332 " " NAGIA 1 " - " ASN Q 448 " " NAGJA 1 " - " ASN Q 276 " Time building additional restraints: 14.44 Conformation dependent library (CDL) restraints added in 5.0 seconds 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7080 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 78 sheets defined 13.7% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.06 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.548A pdb=" N TYR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.952A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.826A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.960A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 Processing helix chain 'B' and resid 570 through 596 removed outlier: 4.187A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 616 removed outlier: 4.310A pdb=" N SER B 615 " --> pdb=" O ASN B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.578A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 663 removed outlier: 3.549A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.904A pdb=" N GLN C 64 " --> pdb=" O ARG C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 removed outlier: 4.112A pdb=" N THR C 87 " --> pdb=" O PRO C 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 100D through 100H Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 57 through 63 removed outlier: 3.548A pdb=" N TYR G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.952A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.827A pdb=" N THR G 373 " --> pdb=" O LEU G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 3.959A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 537 through 543 Processing helix chain 'I' and resid 570 through 596 removed outlier: 4.186A pdb=" N LEU I 581 " --> pdb=" O GLN I 577 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 616 removed outlier: 4.310A pdb=" N SER I 615 " --> pdb=" O ASN I 611 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 623 Processing helix chain 'I' and resid 627 through 636 removed outlier: 3.579A pdb=" N LYS I 633 " --> pdb=" O LEU I 629 " (cutoff:3.500A) Processing helix chain 'I' and resid 641 through 663 removed outlier: 3.550A pdb=" N LEU I 663 " --> pdb=" O ASP I 659 " (cutoff:3.500A) Processing helix chain 'J' and resid 100D through 100H Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'N' and resid 61 through 64 removed outlier: 3.905A pdb=" N GLN N 64 " --> pdb=" O ARG N 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 61 through 64' Processing helix chain 'N' and resid 83 through 87 removed outlier: 4.112A pdb=" N THR N 87 " --> pdb=" O PRO N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'Q' and resid 57 through 63 removed outlier: 3.547A pdb=" N TYR Q 61 " --> pdb=" O ASP Q 57 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 115 Processing helix chain 'Q' and resid 122 through 126 removed outlier: 3.952A pdb=" N CYS Q 126 " --> pdb=" O THR Q 123 " (cutoff:3.500A) Processing helix chain 'Q' and resid 335 through 350 Processing helix chain 'Q' and resid 351 through 353 No H-bonds generated for 'chain 'Q' and resid 351 through 353' Processing helix chain 'Q' and resid 368 through 373 removed outlier: 3.828A pdb=" N THR Q 373 " --> pdb=" O LEU Q 369 " (cutoff:3.500A) Processing helix chain 'Q' and resid 475 through 480 removed outlier: 3.958A pdb=" N TRP Q 479 " --> pdb=" O MET Q 475 " (cutoff:3.500A) Processing helix chain 'R' and resid 529 through 534 Processing helix chain 'R' and resid 537 through 543 Processing helix chain 'R' and resid 570 through 596 removed outlier: 4.185A pdb=" N LEU R 581 " --> pdb=" O GLN R 577 " (cutoff:3.500A) Processing helix chain 'R' and resid 611 through 616 removed outlier: 4.310A pdb=" N SER R 615 " --> pdb=" O ASN R 611 " (cutoff:3.500A) Processing helix chain 'R' and resid 618 through 623 Processing helix chain 'R' and resid 627 through 636 removed outlier: 3.578A pdb=" N LYS R 633 " --> pdb=" O LEU R 629 " (cutoff:3.500A) Processing helix chain 'R' and resid 641 through 663 removed outlier: 3.548A pdb=" N LEU R 663 " --> pdb=" O ASP R 659 " (cutoff:3.500A) Processing helix chain 'S' and resid 100D through 100H Processing helix chain 'T' and resid 79 through 83 Processing helix chain 'V' and resid 61 through 64 removed outlier: 3.905A pdb=" N GLN V 64 " --> pdb=" O ARG V 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 61 through 64' Processing helix chain 'V' and resid 83 through 87 removed outlier: 4.113A pdb=" N THR V 87 " --> pdb=" O PRO V 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 61 through 64 Processing helix chain 'W' and resid 83 through 87 Processing helix chain 'X' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.610A pdb=" N VAL I 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N VAL A 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N THR I 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 47 removed outlier: 4.001A pdb=" N VAL A 44 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.513A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.382A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.068A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.992A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 308 removed outlier: 7.368A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.656A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TRP H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 31 through 31B Processing sheet with id=AB3, first strand: chain 'B' and resid 603 through 609 removed outlier: 7.871A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.521A pdb=" N THR C 70 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.764A pdb=" N VAL C 10 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C 40 " --> pdb=" O PHE C 45 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N PHE C 45 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.764A pdb=" N VAL C 10 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.535A pdb=" N THR D 5 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.391A pdb=" N LEU D 11 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLN D 36 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU D 45 " --> pdb=" O GLN D 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.624A pdb=" N SER E 70 " --> pdb=" O SER E 79 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.834A pdb=" N TYR E 33 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TRP E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR E 50 " --> pdb=" O TRP E 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.753A pdb=" N TYR E 100O" --> pdb=" O LYS E 96 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 99 through 100A Processing sheet with id=AC4, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.089A pdb=" N VAL F 11 " --> pdb=" O ILE F 105 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR F 86 " --> pdb=" O THR F 102 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP F 35 " --> pdb=" O ILE F 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 19 through 23 Processing sheet with id=AC6, first strand: chain 'G' and resid 44 through 47 removed outlier: 4.001A pdb=" N VAL G 44 " --> pdb=" O GLU G 492 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 91 through 94 removed outlier: 3.512A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AC9, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AD1, first strand: chain 'G' and resid 271 through 273 removed outlier: 7.385A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 271 through 273 removed outlier: 11.068A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.589A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 11.992A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 11.650A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.946A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 301 through 308 removed outlier: 7.369A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AD5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD6, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.656A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP O 34 " --> pdb=" O GLY O 50 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 30 through 31B Processing sheet with id=AD8, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.623A pdb=" N SER J 70 " --> pdb=" O SER J 79 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.833A pdb=" N TYR J 33 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.751A pdb=" N TYR J 100O" --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 99 through 100A Processing sheet with id=AE3, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.089A pdb=" N VAL K 11 " --> pdb=" O ILE K 105 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR K 86 " --> pdb=" O THR K 102 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP K 35 " --> pdb=" O ILE K 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'L' and resid 44 through 48 removed outlier: 5.712A pdb=" N LEU L 46 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 44 through 48 removed outlier: 5.712A pdb=" N LEU L 46 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 5 through 6 removed outlier: 3.536A pdb=" N THR M 5 " --> pdb=" O LYS M 24 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.391A pdb=" N LEU M 11 " --> pdb=" O GLU M 100 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN M 36 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU M 45 " --> pdb=" O GLN M 36 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.522A pdb=" N THR N 70 " --> pdb=" O TYR N 79 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.762A pdb=" N VAL N 10 " --> pdb=" O VAL N 110 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE N 40 " --> pdb=" O PHE N 45 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE N 45 " --> pdb=" O ILE N 40 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.762A pdb=" N VAL N 10 " --> pdb=" O VAL N 110 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'P' and resid 44 through 48 removed outlier: 5.711A pdb=" N LEU P 46 " --> pdb=" O LEU P 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 44 through 48 removed outlier: 5.711A pdb=" N LEU P 46 " --> pdb=" O LEU P 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 495 through 499 removed outlier: 5.614A pdb=" N VAL R 608 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N VAL Q 38 " --> pdb=" O THR R 606 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N THR R 606 " --> pdb=" O VAL Q 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 44 through 47 removed outlier: 4.001A pdb=" N VAL Q 44 " --> pdb=" O GLU Q 492 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE Q 225 " --> pdb=" O VAL Q 245 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q' and resid 91 through 94 removed outlier: 3.511A pdb=" N GLU Q 91 " --> pdb=" O CYS Q 239 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 130 through 133 Processing sheet with id=AG3, first strand: chain 'Q' and resid 181 through 183 Processing sheet with id=AG4, first strand: chain 'Q' and resid 271 through 273 removed outlier: 7.385A pdb=" N GLN Q 293 " --> pdb=" O SER Q 334 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER Q 334 " --> pdb=" O GLN Q 293 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Q' and resid 271 through 273 removed outlier: 11.067A pdb=" N VAL Q 286 " --> pdb=" O THR Q 455 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N THR Q 455 " --> pdb=" O VAL Q 286 " (cutoff:3.500A) removed outlier: 11.992A pdb=" N PHE Q 288 " --> pdb=" O ILE Q 453 " (cutoff:3.500A) removed outlier: 11.649A pdb=" N ILE Q 453 " --> pdb=" O PHE Q 288 " (cutoff:3.500A) removed outlier: 10.945A pdb=" N THR Q 290 " --> pdb=" O GLY Q 451 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N GLY Q 451 " --> pdb=" O THR Q 290 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 301 through 308 removed outlier: 7.368A pdb=" N ASN Q 301 " --> pdb=" O ILE Q 322 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE Q 322 " --> pdb=" O ASN Q 301 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR Q 303 " --> pdb=" O GLY Q 321 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 423 through 424 Processing sheet with id=AG8, first strand: chain 'W' and resid 11 through 12 removed outlier: 3.657A pdb=" N VAL W 12 " --> pdb=" O THR W 110 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TRP W 34 " --> pdb=" O GLY W 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY W 50 " --> pdb=" O TRP W 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP W 36 " --> pdb=" O ILE W 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 30 through 31B removed outlier: 6.312A pdb=" N GLY R 516 " --> pdb=" O LYS W 97 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'S' and resid 5 through 7 removed outlier: 3.624A pdb=" N SER S 70 " --> pdb=" O SER S 79 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.834A pdb=" N TYR S 33 " --> pdb=" O THR S 95 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N TYR S 50 " --> pdb=" O TRP S 34 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N TRP S 36 " --> pdb=" O ILE S 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.751A pdb=" N TYR S 100O" --> pdb=" O LYS S 96 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'S' and resid 99 through 100A Processing sheet with id=AH5, first strand: chain 'T' and resid 11 through 13 removed outlier: 6.089A pdb=" N VAL T 11 " --> pdb=" O ILE T 105 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR T 86 " --> pdb=" O THR T 102 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TRP T 35 " --> pdb=" O ILE T 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'T' and resid 19 through 23 Processing sheet with id=AH7, first strand: chain 'U' and resid 5 through 6 removed outlier: 3.535A pdb=" N THR U 5 " --> pdb=" O LYS U 24 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'U' and resid 10 through 13 removed outlier: 6.391A pdb=" N LEU U 11 " --> pdb=" O GLU U 100 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN U 36 " --> pdb=" O LEU U 45 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU U 45 " --> pdb=" O GLN U 36 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'V' and resid 3 through 6 removed outlier: 3.523A pdb=" N THR V 70 " --> pdb=" O TYR V 79 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'V' and resid 10 through 11 removed outlier: 6.763A pdb=" N VAL V 10 " --> pdb=" O VAL V 110 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG V 38 " --> pdb=" O TRP V 47 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TRP V 47 " --> pdb=" O ARG V 38 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE V 40 " --> pdb=" O PHE V 45 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE V 45 " --> pdb=" O ILE V 40 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'V' and resid 10 through 11 removed outlier: 6.763A pdb=" N VAL V 10 " --> pdb=" O VAL V 110 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'W' and resid 3 through 7 Processing sheet with id=AI4, first strand: chain 'X' and resid 4 through 7 Processing sheet with id=AI5, first strand: chain 'X' and resid 44 through 48 removed outlier: 5.714A pdb=" N LEU X 46 " --> pdb=" O LEU X 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU X 37 " --> pdb=" O LEU X 46 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR X 97 " --> pdb=" O GLN X 90 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'X' and resid 44 through 48 removed outlier: 5.714A pdb=" N LEU X 46 " --> pdb=" O LEU X 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU X 37 " --> pdb=" O LEU X 46 " (cutoff:3.500A) 1116 hydrogen bonds defined for protein. 2799 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.87 Time building geometry restraints manager: 15.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9457 1.33 - 1.46: 9333 1.46 - 1.59: 14294 1.59 - 1.72: 0 1.72 - 1.85: 225 Bond restraints: 33309 Sorted by residual: bond pdb=" C1 MAN 6 4 " pdb=" O5 MAN 6 4 " ideal model delta sigma weight residual 1.399 1.481 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C1 MAN q 4 " pdb=" O5 MAN q 4 " ideal model delta sigma weight residual 1.399 1.481 -0.082 2.00e-02 2.50e+03 1.66e+01 bond pdb=" C1 MAN a 4 " pdb=" O5 MAN a 4 " ideal model delta sigma weight residual 1.399 1.480 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C1 NAG 5 1 " pdb=" O5 NAG 5 1 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C1 NAG p 1 " pdb=" O5 NAG p 1 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.55e+01 ... (remaining 33304 not shown) Histogram of bond angle deviations from ideal: 98.14 - 106.16: 928 106.16 - 114.18: 20271 114.18 - 122.21: 17794 122.21 - 130.23: 6073 130.23 - 138.26: 222 Bond angle restraints: 45288 Sorted by residual: angle pdb=" C ASN P 53 " pdb=" N ARG P 54 " pdb=" CA ARG P 54 " ideal model delta sigma weight residual 122.09 130.64 -8.55 1.48e+00 4.57e-01 3.34e+01 angle pdb=" C ASN X 53 " pdb=" N ARG X 54 " pdb=" CA ARG X 54 " ideal model delta sigma weight residual 122.09 130.64 -8.55 1.48e+00 4.57e-01 3.33e+01 angle pdb=" C ASN L 53 " pdb=" N ARG L 54 " pdb=" CA ARG L 54 " ideal model delta sigma weight residual 122.09 130.61 -8.52 1.48e+00 4.57e-01 3.31e+01 angle pdb=" CA LEU W 79 " pdb=" CB LEU W 79 " pdb=" CG LEU W 79 " ideal model delta sigma weight residual 116.30 135.80 -19.50 3.50e+00 8.16e-02 3.10e+01 angle pdb=" CA LEU O 79 " pdb=" CB LEU O 79 " pdb=" CG LEU O 79 " ideal model delta sigma weight residual 116.30 135.75 -19.45 3.50e+00 8.16e-02 3.09e+01 ... (remaining 45283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.94: 20100 23.94 - 47.87: 1384 47.87 - 71.81: 269 71.81 - 95.75: 225 95.75 - 119.68: 159 Dihedral angle restraints: 22137 sinusoidal: 11082 harmonic: 11055 Sorted by residual: dihedral pdb=" CA ASP L 50 " pdb=" C ASP L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta harmonic sigma weight residual -180.00 -119.37 -60.63 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA ASP P 50 " pdb=" C ASP P 50 " pdb=" N VAL P 51 " pdb=" CA VAL P 51 " ideal model delta harmonic sigma weight residual -180.00 -119.38 -60.62 0 5.00e+00 4.00e-02 1.47e+02 dihedral pdb=" CA ASP X 50 " pdb=" C ASP X 50 " pdb=" N VAL X 51 " pdb=" CA VAL X 51 " ideal model delta harmonic sigma weight residual -180.00 -119.47 -60.53 0 5.00e+00 4.00e-02 1.47e+02 ... (remaining 22134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 4401 0.079 - 0.159: 990 0.159 - 0.238: 135 0.238 - 0.318: 45 0.318 - 0.397: 18 Chirality restraints: 5589 Sorted by residual: chirality pdb=" C1 MAN q 4 " pdb=" O3 BMA q 3 " pdb=" C2 MAN q 4 " pdb=" O5 MAN q 4 " both_signs ideal model delta sigma weight residual False 2.40 2.34 0.06 2.00e-02 2.50e+03 8.11e+00 chirality pdb=" C1 MAN 6 4 " pdb=" O3 BMA 6 3 " pdb=" C2 MAN 6 4 " pdb=" O5 MAN 6 4 " both_signs ideal model delta sigma weight residual False 2.40 2.35 0.05 2.00e-02 2.50e+03 6.34e+00 chirality pdb=" C1 MAN a 4 " pdb=" O3 BMA a 3 " pdb=" C2 MAN a 4 " pdb=" O5 MAN a 4 " both_signs ideal model delta sigma weight residual False 2.40 2.35 0.05 2.00e-02 2.50e+03 6.00e+00 ... (remaining 5586 not shown) Planarity restraints: 5565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 28 " 0.091 5.00e-02 4.00e+02 1.40e-01 3.14e+01 pdb=" N PRO H 29 " -0.242 5.00e-02 4.00e+02 pdb=" CA PRO H 29 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO H 29 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR W 28 " -0.091 5.00e-02 4.00e+02 1.40e-01 3.13e+01 pdb=" N PRO W 29 " 0.242 5.00e-02 4.00e+02 pdb=" CA PRO W 29 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO W 29 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR O 28 " 0.091 5.00e-02 4.00e+02 1.40e-01 3.12e+01 pdb=" N PRO O 29 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO O 29 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO O 29 " 0.071 5.00e-02 4.00e+02 ... (remaining 5562 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 7003 2.77 - 3.31: 28556 3.31 - 3.84: 53775 3.84 - 4.37: 59169 4.37 - 4.90: 103109 Nonbonded interactions: 251612 Sorted by model distance: nonbonded pdb=" NH2 ARG W 100F" pdb=" OD2 ASP X 50 " model vdw 2.242 2.520 nonbonded pdb=" OG SER J 70 " pdb=" OG SER J 79 " model vdw 2.244 2.440 nonbonded pdb=" OG SER E 70 " pdb=" OG SER E 79 " model vdw 2.244 2.440 nonbonded pdb=" OG SER S 70 " pdb=" OG SER S 79 " model vdw 2.245 2.440 nonbonded pdb=" OH TYR G 318 " pdb=" OD2 ASP N 76B" model vdw 2.249 2.440 ... (remaining 251607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '4' selection = chain '5' selection = chain 'CA' selection = chain 'DA' selection = chain 'GA' selection = chain 'Y' selection = chain 'Z' selection = chain 'g' selection = chain 'h' selection = chain 'k' selection = chain 'o' selection = chain 'p' selection = chain 'w' selection = chain 'x' } ncs_group { reference = chain '1' selection = chain 'HA' selection = chain 'l' } ncs_group { reference = chain '2' selection = chain '8' selection = chain 'AA' selection = chain 'EA' selection = chain 'IA' selection = chain 'c' selection = chain 'e' selection = chain 'i' selection = chain 'm' selection = chain 's' selection = chain 'u' selection = chain 'y' } ncs_group { reference = chain '3' selection = chain '6' selection = chain '9' selection = chain 'JA' selection = chain 'a' selection = chain 'd' selection = chain 'n' selection = chain 'q' selection = chain 't' } ncs_group { reference = chain '7' selection = chain 'FA' selection = chain 'b' selection = chain 'j' selection = chain 'r' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'Q' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'R' } ncs_group { reference = chain 'BA' selection = chain 'f' selection = chain 'v' } ncs_group { reference = chain 'C' selection = chain 'N' selection = chain 'V' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'U' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'T' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'W' } ncs_group { reference = chain 'L' selection = chain 'P' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 84.900 Find NCS groups from input model: 5.550 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 33309 Z= 0.588 Angle : 1.271 19.499 45288 Z= 0.655 Chirality : 0.072 0.397 5589 Planarity : 0.008 0.140 5508 Dihedral : 21.014 119.682 14904 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.16 % Favored : 93.69 % Rotamer: Outliers : 0.45 % Allowed : 10.44 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.12), residues: 3801 helix: -2.83 (0.18), residues: 369 sheet: -1.25 (0.13), residues: 1269 loop : -2.22 (0.11), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP L 35 HIS 0.007 0.001 HIS E 52 PHE 0.031 0.003 PHE P 91 TYR 0.023 0.003 TYR A 486 ARG 0.012 0.001 ARG W 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 445 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8750 (mtp) cc_final: 0.8536 (mtm) REVERT: B 657 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8157 (tm-30) REVERT: F 20 ARG cc_start: 0.7532 (mpt90) cc_final: 0.7247 (mmt-90) REVERT: F 26 GLU cc_start: 0.8043 (tp30) cc_final: 0.7775 (tp30) REVERT: G 166 ARG cc_start: 0.7314 (mtm110) cc_final: 0.7101 (ttp80) REVERT: G 337 THR cc_start: 0.9384 (OUTLIER) cc_final: 0.9155 (t) REVERT: I 530 MET cc_start: 0.8801 (mtp) cc_final: 0.8587 (mtp) REVERT: I 657 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8128 (tm-30) REVERT: J 75 LYS cc_start: 0.8511 (mttt) cc_final: 0.8220 (tttm) REVERT: J 100 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8289 (tptt) REVERT: K 26 GLU cc_start: 0.8197 (tp30) cc_final: 0.7825 (tp30) REVERT: L 61 ARG cc_start: 0.8362 (mtm180) cc_final: 0.7755 (ttm110) REVERT: L 96 LEU cc_start: 0.7932 (mt) cc_final: 0.6967 (mp) REVERT: L 97 THR cc_start: 0.7604 (m) cc_final: 0.6641 (m) REVERT: O 34 TRP cc_start: 0.8321 (m-10) cc_final: 0.7995 (m-10) REVERT: O 47 TRP cc_start: 0.7803 (t60) cc_final: 0.7031 (t60) REVERT: O 52 THR cc_start: 0.6996 (OUTLIER) cc_final: 0.6296 (m) REVERT: P 96 LEU cc_start: 0.7721 (mt) cc_final: 0.6847 (mp) REVERT: Q 166 ARG cc_start: 0.7323 (mtm110) cc_final: 0.7105 (ttp80) REVERT: Q 337 THR cc_start: 0.9409 (OUTLIER) cc_final: 0.9192 (t) REVERT: R 657 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8053 (tm-30) REVERT: S 75 LYS cc_start: 0.8518 (mttt) cc_final: 0.8260 (tttm) REVERT: T 26 GLU cc_start: 0.8232 (tp30) cc_final: 0.7828 (tp30) REVERT: V 52 LYS cc_start: 0.8787 (mttt) cc_final: 0.8498 (mtpp) REVERT: W 34 TRP cc_start: 0.8816 (m-10) cc_final: 0.8440 (m-10) REVERT: W 52 THR cc_start: 0.7549 (OUTLIER) cc_final: 0.7216 (m) REVERT: X 91 PHE cc_start: 0.8515 (p90) cc_final: 0.7909 (p90) REVERT: X 96 LEU cc_start: 0.7876 (mt) cc_final: 0.7085 (mt) REVERT: X 98 PHE cc_start: 0.7157 (m-80) cc_final: 0.6865 (m-80) outliers start: 15 outliers final: 2 residues processed: 460 average time/residue: 0.5355 time to fit residues: 366.6417 Evaluate side-chains 240 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 234 time to evaluate : 3.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain W residue 52 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 6.9990 chunk 286 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 193 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 chunk 296 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 343 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 203 GLN A 246 GLN A 328 GLN A 411 ASN B 543 ASN C 64 GLN C 72 GLN D 27 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN F 51 ASN G 72 HIS G 82 GLN G 183 GLN G 203 GLN G 246 GLN G 328 GLN G 411 ASN H 39 GLN H 76 ASN I 543 ASN J 5 GLN J 58 ASN K 51 ASN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN M 27 GLN ** M 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 64 GLN N 72 GLN O 76 ASN P 27 GLN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN Q 82 GLN Q 203 GLN Q 246 GLN Q 328 GLN Q 411 ASN R 543 ASN S 58 ASN T 51 ASN U 27 GLN U 36 GLN V 64 GLN V 72 GLN W 39 GLN W 76 ASN ** X 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 53 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 33309 Z= 0.306 Angle : 0.785 9.835 45288 Z= 0.379 Chirality : 0.049 0.299 5589 Planarity : 0.005 0.079 5508 Dihedral : 17.565 112.340 7924 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.08 % Favored : 94.82 % Rotamer: Outliers : 2.21 % Allowed : 15.83 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.12), residues: 3801 helix: -0.94 (0.25), residues: 363 sheet: -0.89 (0.14), residues: 1239 loop : -1.82 (0.12), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 571 HIS 0.005 0.001 HIS G 66 PHE 0.022 0.002 PHE M 92 TYR 0.026 0.002 TYR J 33 ARG 0.007 0.001 ARG O 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 261 time to evaluate : 3.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 657 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8214 (tm-30) REVERT: F 20 ARG cc_start: 0.7437 (mpt90) cc_final: 0.7028 (mmt-90) REVERT: G 166 ARG cc_start: 0.7467 (mtm110) cc_final: 0.7263 (ttp80) REVERT: G 215 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9137 (pt) REVERT: H 34 TRP cc_start: 0.8104 (m-10) cc_final: 0.7601 (m-10) REVERT: I 657 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8175 (tm-30) REVERT: J 73 LYS cc_start: 0.7348 (tptt) cc_final: 0.6912 (tppt) REVERT: J 75 LYS cc_start: 0.8563 (mttt) cc_final: 0.8334 (tttm) REVERT: J 100 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8437 (tptt) REVERT: K 13 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7627 (t) REVERT: L 4 MET cc_start: 0.5319 (mmm) cc_final: 0.5042 (mmm) REVERT: L 30 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8186 (p0) REVERT: L 39 LYS cc_start: 0.5750 (mppt) cc_final: 0.5214 (mtpp) REVERT: L 89 MET cc_start: 0.8305 (tmm) cc_final: 0.7863 (tmm) REVERT: L 94 PHE cc_start: 0.7786 (m-80) cc_final: 0.7522 (m-80) REVERT: L 97 THR cc_start: 0.7448 (m) cc_final: 0.7196 (p) REVERT: O 1 GLN cc_start: 0.3479 (pp30) cc_final: 0.2274 (pm20) REVERT: O 34 TRP cc_start: 0.8141 (m-10) cc_final: 0.7590 (m-10) REVERT: O 47 TRP cc_start: 0.7432 (t60) cc_final: 0.6888 (t60) REVERT: P 89 MET cc_start: 0.8178 (tmm) cc_final: 0.7639 (tmm) REVERT: P 97 THR cc_start: 0.7647 (m) cc_final: 0.7391 (p) REVERT: R 657 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8139 (tm-30) REVERT: S 75 LYS cc_start: 0.8532 (mttt) cc_final: 0.8262 (tttm) REVERT: V 52 LYS cc_start: 0.8750 (mttt) cc_final: 0.8460 (mtpp) REVERT: X 4 MET cc_start: 0.5628 (mmm) cc_final: 0.5413 (mmm) REVERT: X 61 ARG cc_start: 0.8477 (ptp90) cc_final: 0.8078 (ptp90) REVERT: X 77 ARG cc_start: 0.9065 (tmt170) cc_final: 0.8702 (tmt170) REVERT: X 89 MET cc_start: 0.7533 (tmm) cc_final: 0.7316 (tmm) REVERT: X 97 THR cc_start: 0.7801 (m) cc_final: 0.7510 (p) outliers start: 74 outliers final: 33 residues processed: 317 average time/residue: 0.5095 time to fit residues: 248.5783 Evaluate side-chains 246 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 210 time to evaluate : 4.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 245 VAL Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain V residue 100 ASP Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain X residue 7 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 285 optimal weight: 0.0980 chunk 233 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 343 optimal weight: 4.9990 chunk 371 optimal weight: 40.0000 chunk 306 optimal weight: 4.9990 chunk 341 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 275 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN B 543 ASN B 577 GLN B 590 GLN C 101 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS H 76 ASN I 543 ASN I 577 GLN J 97 HIS ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN M 36 GLN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN ** Q 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 183 GLN Q 411 ASN R 543 ASN R 577 GLN S 97 HIS V 101 GLN X 27 GLN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 33309 Z= 0.338 Angle : 0.774 13.478 45288 Z= 0.370 Chirality : 0.049 0.280 5589 Planarity : 0.005 0.069 5508 Dihedral : 15.160 113.261 7920 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.02 % Favored : 93.87 % Rotamer: Outliers : 4.29 % Allowed : 15.62 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.13), residues: 3801 helix: 0.09 (0.27), residues: 366 sheet: -0.70 (0.14), residues: 1245 loop : -1.61 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 571 HIS 0.003 0.001 HIS A 330 PHE 0.026 0.002 PHE P 62 TYR 0.021 0.002 TYR X 49 ARG 0.007 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 229 time to evaluate : 3.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 657 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8242 (tm-30) REVERT: F 13 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.8047 (t) REVERT: F 20 ARG cc_start: 0.7348 (mpt90) cc_final: 0.6902 (mmt-90) REVERT: G 166 ARG cc_start: 0.7451 (mtm110) cc_final: 0.7215 (ttp80) REVERT: G 288 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8579 (p90) REVERT: I 657 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8201 (tm-30) REVERT: J 75 LYS cc_start: 0.8576 (mttt) cc_final: 0.8292 (tttm) REVERT: J 100 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8490 (tptt) REVERT: L 24 ARG cc_start: 0.8695 (tpp80) cc_final: 0.8241 (mmm-85) REVERT: L 30 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8185 (p0) REVERT: L 39 LYS cc_start: 0.5879 (mppt) cc_final: 0.5482 (mtpp) REVERT: L 97 THR cc_start: 0.7319 (m) cc_final: 0.6942 (p) REVERT: O 1 GLN cc_start: 0.3507 (pp30) cc_final: 0.2584 (pm20) REVERT: O 34 TRP cc_start: 0.8230 (m-10) cc_final: 0.7897 (m-10) REVERT: O 53 ASN cc_start: 0.8801 (t0) cc_final: 0.8583 (p0) REVERT: O 82 LEU cc_start: 0.4569 (OUTLIER) cc_final: 0.4320 (tt) REVERT: P 39 LYS cc_start: 0.6595 (mppt) cc_final: 0.5708 (mtpp) REVERT: P 82 ASP cc_start: 0.5439 (OUTLIER) cc_final: 0.5142 (p0) REVERT: P 97 THR cc_start: 0.7256 (OUTLIER) cc_final: 0.6882 (p) REVERT: Q 337 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.9144 (t) REVERT: R 657 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8183 (tm-30) REVERT: S 20 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8259 (tt) REVERT: X 70 ASP cc_start: 0.8783 (t0) cc_final: 0.8449 (p0) REVERT: X 77 ARG cc_start: 0.9119 (tmt170) cc_final: 0.8688 (tmt170) REVERT: X 97 THR cc_start: 0.7900 (m) cc_final: 0.7456 (p) outliers start: 144 outliers final: 64 residues processed: 356 average time/residue: 0.4571 time to fit residues: 258.4403 Evaluate side-chains 272 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 200 time to evaluate : 3.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 88 ASN Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain Q residue 245 VAL Chi-restraints excluded: chain Q residue 270 VAL Chi-restraints excluded: chain Q residue 337 THR Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 424 ILE Chi-restraints excluded: chain Q residue 426 MET Chi-restraints excluded: chain Q residue 491 ILE Chi-restraints excluded: chain R residue 536 THR Chi-restraints excluded: chain R residue 539 VAL Chi-restraints excluded: chain R residue 604 CYS Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain V residue 51 ILE Chi-restraints excluded: chain V residue 109 VAL Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 53 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 8.9990 chunk 258 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 230 optimal weight: 20.0000 chunk 345 optimal weight: 0.8980 chunk 365 optimal weight: 8.9990 chunk 180 optimal weight: 7.9990 chunk 327 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN A 411 ASN B 543 ASN ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 543 ASN ** I 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 53 ASN M 36 GLN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 27 GLN ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 53 ASN ** Q 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 411 ASN R 543 ASN ** R 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 GLN W 53 ASN ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 33309 Z= 0.437 Angle : 0.803 10.447 45288 Z= 0.386 Chirality : 0.050 0.273 5589 Planarity : 0.005 0.064 5508 Dihedral : 13.653 115.231 7920 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.89 % Favored : 93.05 % Rotamer: Outliers : 4.20 % Allowed : 17.62 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3801 helix: 0.31 (0.27), residues: 363 sheet: -0.67 (0.14), residues: 1236 loop : -1.59 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 571 HIS 0.005 0.001 HIS A 330 PHE 0.039 0.002 PHE P 98 TYR 0.019 0.002 TYR C 32 ARG 0.006 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 215 time to evaluate : 4.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9002 (tt) REVERT: B 657 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8298 (tm-30) REVERT: E 13 LYS cc_start: 0.9225 (mmmt) cc_final: 0.8542 (mmmt) REVERT: E 16 GLU cc_start: 0.7519 (pt0) cc_final: 0.7115 (mp0) REVERT: F 20 ARG cc_start: 0.7323 (mpt90) cc_final: 0.6863 (mmt-90) REVERT: G 125 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8911 (tt) REVERT: G 288 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8561 (p90) REVERT: H 34 TRP cc_start: 0.8345 (m-10) cc_final: 0.7905 (m-10) REVERT: I 657 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8249 (tm-30) REVERT: J 100 LYS cc_start: 0.8956 (mmmt) cc_final: 0.8514 (tptt) REVERT: L 30 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8307 (p0) REVERT: L 70 ASP cc_start: 0.8931 (t0) cc_final: 0.8632 (p0) REVERT: L 77 ARG cc_start: 0.8988 (tmt170) cc_final: 0.8764 (tmt170) REVERT: L 97 THR cc_start: 0.7034 (m) cc_final: 0.6581 (p) REVERT: O 1 GLN cc_start: 0.3729 (pp30) cc_final: 0.2745 (pm20) REVERT: O 34 TRP cc_start: 0.8404 (m-10) cc_final: 0.8066 (m-10) REVERT: O 53 ASN cc_start: 0.8819 (t0) cc_final: 0.8510 (p0) REVERT: P 82 ASP cc_start: 0.5586 (OUTLIER) cc_final: 0.5305 (p0) REVERT: R 657 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8237 (tm-30) REVERT: S 13 LYS cc_start: 0.9235 (mmmt) cc_final: 0.8526 (mmmt) REVERT: S 16 GLU cc_start: 0.7606 (pt0) cc_final: 0.6778 (mp0) REVERT: S 20 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8371 (tt) REVERT: V 76 ASP cc_start: 0.8458 (m-30) cc_final: 0.8225 (t70) REVERT: W 1 GLN cc_start: 0.3550 (pm20) cc_final: 0.3299 (pm20) REVERT: X 77 ARG cc_start: 0.9248 (tmt170) cc_final: 0.8837 (tmt170) REVERT: X 97 THR cc_start: 0.7873 (m) cc_final: 0.7323 (p) outliers start: 141 outliers final: 80 residues processed: 326 average time/residue: 0.4549 time to fit residues: 240.5546 Evaluate side-chains 280 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 194 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 60 ASN Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 88 ASN Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 135 THR Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain Q residue 245 VAL Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 424 ILE Chi-restraints excluded: chain Q residue 426 MET Chi-restraints excluded: chain Q residue 491 ILE Chi-restraints excluded: chain R residue 535 MET Chi-restraints excluded: chain R residue 536 THR Chi-restraints excluded: chain R residue 539 VAL Chi-restraints excluded: chain R residue 593 LEU Chi-restraints excluded: chain R residue 604 CYS Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain V residue 51 ILE Chi-restraints excluded: chain V residue 109 VAL Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 53 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 272 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 311 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 186 optimal weight: 10.0000 chunk 327 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 411 ASN B 543 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 543 ASN L 53 ASN M 36 GLN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 HIS R 543 ASN ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33309 Z= 0.218 Angle : 0.713 13.806 45288 Z= 0.338 Chirality : 0.047 0.281 5589 Planarity : 0.005 0.056 5508 Dihedral : 12.585 111.459 7920 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.05 % Rotamer: Outliers : 3.49 % Allowed : 18.66 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 3801 helix: 0.70 (0.28), residues: 363 sheet: -0.65 (0.14), residues: 1296 loop : -1.37 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP W 103 HIS 0.002 0.001 HIS Q 66 PHE 0.021 0.002 PHE H 78 TYR 0.036 0.001 TYR P 87 ARG 0.004 0.000 ARG P 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 218 time to evaluate : 3.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8982 (tt) REVERT: B 657 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8270 (tm-30) REVERT: E 13 LYS cc_start: 0.9192 (mmmt) cc_final: 0.8541 (mmmt) REVERT: E 16 GLU cc_start: 0.7418 (pt0) cc_final: 0.7041 (mp0) REVERT: F 13 VAL cc_start: 0.8414 (OUTLIER) cc_final: 0.8214 (t) REVERT: G 125 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8938 (tt) REVERT: G 288 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8620 (p90) REVERT: H 33 TYR cc_start: 0.6099 (t80) cc_final: 0.5444 (t80) REVERT: H 34 TRP cc_start: 0.8334 (m-10) cc_final: 0.7904 (m-10) REVERT: I 657 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8206 (tm-30) REVERT: J 100 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8507 (tmtt) REVERT: L 30 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8285 (p0) REVERT: L 39 LYS cc_start: 0.6427 (mptt) cc_final: 0.5671 (mtpp) REVERT: L 77 ARG cc_start: 0.8958 (tmt170) cc_final: 0.8464 (tmt170) REVERT: L 89 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7749 (tpp) REVERT: L 97 THR cc_start: 0.7176 (m) cc_final: 0.6927 (p) REVERT: N 76 ASP cc_start: 0.8506 (m-30) cc_final: 0.8114 (t70) REVERT: O 33 TYR cc_start: 0.6024 (t80) cc_final: 0.5547 (t80) REVERT: O 34 TRP cc_start: 0.8414 (m-10) cc_final: 0.7995 (m-10) REVERT: O 53 ASN cc_start: 0.8792 (t0) cc_final: 0.8496 (p0) REVERT: P 13 VAL cc_start: 0.6033 (OUTLIER) cc_final: 0.5735 (t) REVERT: P 82 ASP cc_start: 0.5402 (OUTLIER) cc_final: 0.5148 (p0) REVERT: R 657 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8179 (tm-30) REVERT: S 13 LYS cc_start: 0.9220 (mmmt) cc_final: 0.8595 (mmmt) REVERT: S 16 GLU cc_start: 0.7662 (pt0) cc_final: 0.7088 (mp0) REVERT: S 20 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8456 (tt) REVERT: W 1 GLN cc_start: 0.3516 (pm20) cc_final: 0.3298 (pm20) REVERT: W 31 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8355 (ptp90) REVERT: W 103 TRP cc_start: 0.7290 (m-10) cc_final: 0.6996 (m-10) REVERT: X 70 ASP cc_start: 0.9010 (t0) cc_final: 0.8669 (p0) REVERT: X 77 ARG cc_start: 0.9269 (tmt170) cc_final: 0.9044 (tpt-90) outliers start: 117 outliers final: 70 residues processed: 308 average time/residue: 0.4273 time to fit residues: 213.6993 Evaluate side-chains 284 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 204 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 89 MET Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain Q residue 88 ASN Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 424 ILE Chi-restraints excluded: chain Q residue 426 MET Chi-restraints excluded: chain Q residue 491 ILE Chi-restraints excluded: chain R residue 535 MET Chi-restraints excluded: chain R residue 536 THR Chi-restraints excluded: chain R residue 539 VAL Chi-restraints excluded: chain R residue 593 LEU Chi-restraints excluded: chain R residue 604 CYS Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain V residue 100 ASP Chi-restraints excluded: chain V residue 109 VAL Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 31 ARG Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 53 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 7.9990 chunk 329 optimal weight: 10.0000 chunk 72 optimal weight: 0.5980 chunk 214 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 365 optimal weight: 10.0000 chunk 303 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 192 optimal weight: 9.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 411 ASN B 543 ASN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 36 GLN ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 HIS R 543 ASN ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 33309 Z= 0.346 Angle : 0.750 15.555 45288 Z= 0.356 Chirality : 0.047 0.288 5589 Planarity : 0.005 0.052 5508 Dihedral : 12.163 113.188 7920 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.92 % Favored : 93.05 % Rotamer: Outliers : 4.00 % Allowed : 19.26 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.13), residues: 3801 helix: 0.73 (0.27), residues: 366 sheet: -0.61 (0.14), residues: 1281 loop : -1.35 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP T 96 HIS 0.005 0.001 HIS A 72 PHE 0.018 0.002 PHE O 78 TYR 0.019 0.002 TYR L 87 ARG 0.005 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 205 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9043 (tt) REVERT: B 657 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8304 (tm-30) REVERT: E 13 LYS cc_start: 0.9225 (mmmt) cc_final: 0.8456 (tptp) REVERT: E 16 GLU cc_start: 0.7530 (pt0) cc_final: 0.7070 (mp0) REVERT: G 125 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8971 (tt) REVERT: G 288 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8564 (p90) REVERT: H 33 TYR cc_start: 0.6061 (t80) cc_final: 0.5445 (t80) REVERT: H 34 TRP cc_start: 0.8497 (m-10) cc_final: 0.8095 (m-10) REVERT: I 657 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8260 (tm-30) REVERT: J 100 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8522 (tptt) REVERT: L 39 LYS cc_start: 0.6458 (mptt) cc_final: 0.5729 (mtpp) REVERT: L 77 ARG cc_start: 0.8926 (tmt170) cc_final: 0.8491 (tmt170) REVERT: N 76 ASP cc_start: 0.8511 (m-30) cc_final: 0.8006 (t0) REVERT: O 1 GLN cc_start: 0.3941 (pm20) cc_final: 0.3684 (pm20) REVERT: O 33 TYR cc_start: 0.6053 (t80) cc_final: 0.5626 (t80) REVERT: O 34 TRP cc_start: 0.8461 (m-10) cc_final: 0.8072 (m-10) REVERT: O 86 ASP cc_start: 0.0976 (p0) cc_final: 0.0725 (p0) REVERT: P 13 VAL cc_start: 0.6018 (OUTLIER) cc_final: 0.5693 (t) REVERT: P 82 ASP cc_start: 0.5388 (OUTLIER) cc_final: 0.5125 (p0) REVERT: R 657 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8220 (tm-30) REVERT: S 13 LYS cc_start: 0.9251 (mmmt) cc_final: 0.8607 (mmmt) REVERT: S 16 GLU cc_start: 0.7750 (pt0) cc_final: 0.7091 (mp0) REVERT: S 20 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8530 (tt) REVERT: W 1 GLN cc_start: 0.3673 (pm20) cc_final: 0.3446 (pm20) REVERT: W 31 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8321 (ptp90) REVERT: W 39 GLN cc_start: 0.6328 (tt0) cc_final: 0.6089 (tm-30) REVERT: W 103 TRP cc_start: 0.7308 (m-10) cc_final: 0.7039 (m-10) REVERT: X 70 ASP cc_start: 0.9028 (t0) cc_final: 0.8735 (p0) outliers start: 134 outliers final: 94 residues processed: 313 average time/residue: 0.4146 time to fit residues: 212.0374 Evaluate side-chains 300 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 199 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 593 LEU Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain M residue 36 GLN Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 89 MET Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 88 ASN Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 260 LEU Chi-restraints excluded: chain Q residue 345 VAL Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 424 ILE Chi-restraints excluded: chain Q residue 491 ILE Chi-restraints excluded: chain R residue 535 MET Chi-restraints excluded: chain R residue 536 THR Chi-restraints excluded: chain R residue 539 VAL Chi-restraints excluded: chain R residue 593 LEU Chi-restraints excluded: chain R residue 604 CYS Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain U residue 3 VAL Chi-restraints excluded: chain V residue 100 ASP Chi-restraints excluded: chain V residue 109 VAL Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 31 ARG Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 53 ASN Chi-restraints excluded: chain X residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 307 optimal weight: 4.9990 chunk 204 optimal weight: 30.0000 chunk 364 optimal weight: 20.0000 chunk 228 optimal weight: 1.9990 chunk 222 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 411 ASN D 27 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 HIS R 543 ASN U 27 GLN ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 33309 Z= 0.345 Angle : 0.756 15.468 45288 Z= 0.358 Chirality : 0.047 0.291 5589 Planarity : 0.005 0.053 5508 Dihedral : 11.746 113.661 7920 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 4.44 % Allowed : 19.23 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.13), residues: 3801 helix: 0.78 (0.28), residues: 366 sheet: -0.61 (0.14), residues: 1287 loop : -1.31 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Q 96 HIS 0.003 0.001 HIS A 330 PHE 0.023 0.002 PHE L 98 TYR 0.023 0.002 TYR P 87 ARG 0.004 0.000 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 212 time to evaluate : 3.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9011 (tt) REVERT: B 657 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8293 (tm-30) REVERT: E 16 GLU cc_start: 0.7550 (pt0) cc_final: 0.7134 (mp0) REVERT: G 125 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8983 (tt) REVERT: G 288 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8536 (p90) REVERT: H 33 TYR cc_start: 0.6013 (t80) cc_final: 0.5453 (t80) REVERT: H 34 TRP cc_start: 0.8569 (m-10) cc_final: 0.8034 (m-10) REVERT: I 657 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8267 (tm-30) REVERT: J 100 LYS cc_start: 0.8967 (mmmt) cc_final: 0.8509 (tptt) REVERT: L 24 ARG cc_start: 0.8499 (mmm-85) cc_final: 0.8189 (mmt-90) REVERT: L 39 LYS cc_start: 0.6283 (mptt) cc_final: 0.5574 (mtmm) REVERT: L 70 ASP cc_start: 0.8998 (t0) cc_final: 0.8676 (t0) REVERT: L 77 ARG cc_start: 0.8973 (tmt170) cc_final: 0.8559 (tmt170) REVERT: L 97 THR cc_start: 0.7024 (m) cc_final: 0.6732 (p) REVERT: O 1 GLN cc_start: 0.3797 (pm20) cc_final: 0.3452 (pm20) REVERT: O 33 TYR cc_start: 0.6064 (t80) cc_final: 0.5639 (t80) REVERT: O 34 TRP cc_start: 0.8523 (m-10) cc_final: 0.8076 (m-10) REVERT: O 86 ASP cc_start: 0.1011 (p0) cc_final: 0.0761 (p0) REVERT: P 13 VAL cc_start: 0.5979 (OUTLIER) cc_final: 0.5650 (t) REVERT: P 27 GLN cc_start: 0.8564 (tp-100) cc_final: 0.8219 (tp-100) REVERT: P 82 ASP cc_start: 0.5445 (OUTLIER) cc_final: 0.5146 (p0) REVERT: Q 273 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8513 (mtt-85) REVERT: R 530 MET cc_start: 0.8836 (mmm) cc_final: 0.8506 (mmt) REVERT: R 657 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8177 (tm-30) REVERT: S 16 GLU cc_start: 0.7752 (pt0) cc_final: 0.6945 (mp0) REVERT: S 20 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8600 (tt) REVERT: S 80 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8163 (pp) REVERT: U 32 MET cc_start: 0.8203 (tpp) cc_final: 0.7340 (ttt) REVERT: W 1 GLN cc_start: 0.3708 (OUTLIER) cc_final: 0.2707 (pm20) REVERT: W 31 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8322 (ptp90) REVERT: X 13 VAL cc_start: 0.6658 (OUTLIER) cc_final: 0.6408 (t) REVERT: X 70 ASP cc_start: 0.8992 (t0) cc_final: 0.8621 (p0) outliers start: 149 outliers final: 108 residues processed: 335 average time/residue: 0.4611 time to fit residues: 250.9330 Evaluate side-chains 321 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 202 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 163 THR Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 345 VAL Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 593 LEU Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 89 MET Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 17 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain O residue 60 ASN Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 89 MET Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 88 ASN Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 135 THR Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 260 LEU Chi-restraints excluded: chain Q residue 273 ARG Chi-restraints excluded: chain Q residue 323 ILE Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 424 ILE Chi-restraints excluded: chain Q residue 448 ASN Chi-restraints excluded: chain Q residue 491 ILE Chi-restraints excluded: chain R residue 536 THR Chi-restraints excluded: chain R residue 539 VAL Chi-restraints excluded: chain R residue 593 LEU Chi-restraints excluded: chain R residue 604 CYS Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 80 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain V residue 51 ILE Chi-restraints excluded: chain V residue 100 ASP Chi-restraints excluded: chain V residue 109 VAL Chi-restraints excluded: chain W residue 1 GLN Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 31 ARG Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 53 ASN Chi-restraints excluded: chain X residue 89 MET Chi-restraints excluded: chain X residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 109 optimal weight: 0.0570 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 231 optimal weight: 0.6980 chunk 248 optimal weight: 10.0000 chunk 180 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 286 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 HIS ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33309 Z= 0.176 Angle : 0.713 14.441 45288 Z= 0.334 Chirality : 0.046 0.285 5589 Planarity : 0.004 0.053 5508 Dihedral : 10.985 109.918 7920 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.62 % Allowed : 21.26 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3801 helix: 1.05 (0.28), residues: 363 sheet: -0.39 (0.14), residues: 1266 loop : -1.17 (0.14), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP W 103 HIS 0.005 0.001 HIS Q 72 PHE 0.018 0.001 PHE W 78 TYR 0.026 0.001 TYR P 87 ARG 0.010 0.000 ARG X 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 224 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 657 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8243 (tm-30) REVERT: E 13 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8457 (tptp) REVERT: E 16 GLU cc_start: 0.7368 (pt0) cc_final: 0.6936 (mp0) REVERT: G 125 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8962 (tt) REVERT: G 288 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8622 (p90) REVERT: H 33 TYR cc_start: 0.6022 (t80) cc_final: 0.5569 (t80) REVERT: H 34 TRP cc_start: 0.8628 (m-10) cc_final: 0.8131 (m-10) REVERT: I 657 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8223 (tm-30) REVERT: J 100 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8516 (tmtt) REVERT: L 24 ARG cc_start: 0.8492 (mmm-85) cc_final: 0.8192 (mmt-90) REVERT: L 70 ASP cc_start: 0.8956 (t0) cc_final: 0.8680 (t0) REVERT: L 77 ARG cc_start: 0.8987 (tmt170) cc_final: 0.8518 (tmt170) REVERT: N 76 ASP cc_start: 0.8511 (m-30) cc_final: 0.8249 (t70) REVERT: O 1 GLN cc_start: 0.3627 (pm20) cc_final: 0.3263 (pm20) REVERT: O 33 TYR cc_start: 0.6061 (t80) cc_final: 0.5673 (t80) REVERT: O 34 TRP cc_start: 0.8525 (m-10) cc_final: 0.8109 (m-10) REVERT: O 86 ASP cc_start: 0.1096 (p0) cc_final: 0.0826 (p0) REVERT: P 27 GLN cc_start: 0.8541 (tp-100) cc_final: 0.8256 (tp40) REVERT: P 93 GLU cc_start: 0.8288 (tp30) cc_final: 0.8034 (tp30) REVERT: R 530 MET cc_start: 0.8790 (mmm) cc_final: 0.8276 (mmt) REVERT: R 657 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8155 (tm-30) REVERT: S 13 LYS cc_start: 0.9227 (mmmt) cc_final: 0.8400 (tptp) REVERT: S 16 GLU cc_start: 0.7625 (pt0) cc_final: 0.7021 (mp0) REVERT: U 32 MET cc_start: 0.8024 (tpp) cc_final: 0.7741 (ttt) REVERT: W 1 GLN cc_start: 0.3631 (OUTLIER) cc_final: 0.3430 (pm20) REVERT: W 31 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8359 (ptp90) REVERT: W 39 GLN cc_start: 0.6477 (tt0) cc_final: 0.6198 (tm-30) outliers start: 88 outliers final: 66 residues processed: 289 average time/residue: 0.4477 time to fit residues: 205.9693 Evaluate side-chains 275 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 205 time to evaluate : 3.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 604 CYS Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 89 MET Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 89 MET Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 242 VAL Chi-restraints excluded: chain Q residue 260 LEU Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 424 ILE Chi-restraints excluded: chain Q residue 491 ILE Chi-restraints excluded: chain R residue 539 VAL Chi-restraints excluded: chain R residue 573 ILE Chi-restraints excluded: chain R residue 604 CYS Chi-restraints excluded: chain V residue 100 ASP Chi-restraints excluded: chain V residue 109 VAL Chi-restraints excluded: chain W residue 1 GLN Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 31 ARG Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 60 ASP Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 89 MET Chi-restraints excluded: chain X residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 5.9990 chunk 349 optimal weight: 4.9990 chunk 318 optimal weight: 7.9990 chunk 339 optimal weight: 9.9990 chunk 348 optimal weight: 3.9990 chunk 204 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 chunk 266 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 306 optimal weight: 6.9990 chunk 321 optimal weight: 3.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 HIS ** R 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 33309 Z= 0.489 Angle : 0.831 14.389 45288 Z= 0.398 Chirality : 0.049 0.289 5589 Planarity : 0.005 0.054 5508 Dihedral : 11.110 115.262 7920 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 3.19 % Allowed : 21.02 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3801 helix: 0.75 (0.28), residues: 366 sheet: -0.49 (0.14), residues: 1269 loop : -1.32 (0.14), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP W 103 HIS 0.003 0.001 HIS G 352 PHE 0.024 0.002 PHE G 288 TYR 0.025 0.002 TYR N 32 ARG 0.006 0.001 ARG W 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 208 time to evaluate : 3.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 657 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8322 (tm-30) REVERT: E 13 LYS cc_start: 0.9269 (mmmt) cc_final: 0.8373 (tptp) REVERT: E 16 GLU cc_start: 0.7515 (pt0) cc_final: 0.6837 (mp0) REVERT: G 125 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8988 (tt) REVERT: G 288 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8516 (p90) REVERT: H 33 TYR cc_start: 0.6042 (t80) cc_final: 0.5546 (t80) REVERT: H 34 TRP cc_start: 0.8739 (m-10) cc_final: 0.8221 (m-10) REVERT: H 86 ASP cc_start: 0.0426 (p0) cc_final: 0.0182 (p0) REVERT: I 657 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8330 (tm-30) REVERT: J 100 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8535 (tptt) REVERT: L 77 ARG cc_start: 0.8967 (tmt170) cc_final: 0.8517 (tmt170) REVERT: L 98 PHE cc_start: 0.5422 (OUTLIER) cc_final: 0.5043 (t80) REVERT: M 32 MET cc_start: 0.8329 (tpp) cc_final: 0.7734 (ttt) REVERT: N 76 ASP cc_start: 0.8503 (m-30) cc_final: 0.8210 (t70) REVERT: O 1 GLN cc_start: 0.3789 (pm20) cc_final: 0.3450 (pm20) REVERT: O 33 TYR cc_start: 0.6001 (t80) cc_final: 0.5637 (t80) REVERT: O 34 TRP cc_start: 0.8683 (m-10) cc_final: 0.8053 (m-90) REVERT: O 86 ASP cc_start: 0.1234 (p0) cc_final: 0.0920 (p0) REVERT: P 13 VAL cc_start: 0.5744 (OUTLIER) cc_final: 0.5394 (t) REVERT: P 27 GLN cc_start: 0.8528 (tp-100) cc_final: 0.8272 (tp-100) REVERT: Q 273 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8511 (mtt-85) REVERT: Q 288 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8710 (p90) REVERT: R 530 MET cc_start: 0.8736 (mmm) cc_final: 0.8513 (mmt) REVERT: R 657 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8245 (tm-30) REVERT: S 13 LYS cc_start: 0.9279 (mmmt) cc_final: 0.8397 (tptp) REVERT: S 16 GLU cc_start: 0.7760 (pt0) cc_final: 0.6856 (mp0) REVERT: W 1 GLN cc_start: 0.3883 (OUTLIER) cc_final: 0.2886 (pm20) REVERT: W 31 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8289 (ptp90) REVERT: W 39 GLN cc_start: 0.6516 (tt0) cc_final: 0.6105 (tm-30) REVERT: W 86 ASP cc_start: -0.0050 (p0) cc_final: -0.0500 (p0) REVERT: X 13 VAL cc_start: 0.6136 (OUTLIER) cc_final: 0.5906 (t) outliers start: 107 outliers final: 83 residues processed: 295 average time/residue: 0.4641 time to fit residues: 220.6734 Evaluate side-chains 293 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 201 time to evaluate : 3.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 416 LEU Chi-restraints excluded: chain G residue 448 ASN Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain I residue 536 THR Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 89 MET Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain N residue 13 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 89 MET Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 260 LEU Chi-restraints excluded: chain Q residue 273 ARG Chi-restraints excluded: chain Q residue 288 PHE Chi-restraints excluded: chain Q residue 323 ILE Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 424 ILE Chi-restraints excluded: chain Q residue 448 ASN Chi-restraints excluded: chain Q residue 491 ILE Chi-restraints excluded: chain R residue 536 THR Chi-restraints excluded: chain R residue 539 VAL Chi-restraints excluded: chain R residue 573 ILE Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain S residue 95 THR Chi-restraints excluded: chain S residue 100 VAL Chi-restraints excluded: chain V residue 51 ILE Chi-restraints excluded: chain V residue 109 VAL Chi-restraints excluded: chain W residue 1 GLN Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 31 ARG Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain X residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 0.0770 chunk 222 optimal weight: 0.9990 chunk 359 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 249 optimal weight: 30.0000 chunk 376 optimal weight: 9.9990 chunk 346 optimal weight: 0.7980 chunk 299 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 231 optimal weight: 0.5980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 577 GLN L 42 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 HIS R 543 ASN R 577 GLN ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33309 Z= 0.180 Angle : 0.717 14.276 45288 Z= 0.339 Chirality : 0.046 0.286 5589 Planarity : 0.004 0.051 5508 Dihedral : 10.244 110.842 7920 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.24 % Allowed : 22.00 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3801 helix: 1.21 (0.29), residues: 345 sheet: -0.37 (0.14), residues: 1269 loop : -1.12 (0.14), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP W 103 HIS 0.004 0.001 HIS A 72 PHE 0.017 0.001 PHE H 78 TYR 0.021 0.001 TYR P 87 ARG 0.006 0.000 ARG X 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 217 time to evaluate : 3.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 657 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8252 (tm-30) REVERT: E 13 LYS cc_start: 0.9191 (mmmt) cc_final: 0.8482 (tptp) REVERT: E 16 GLU cc_start: 0.7393 (pt0) cc_final: 0.6979 (mp0) REVERT: G 125 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8975 (tt) REVERT: G 288 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8663 (p90) REVERT: H 33 TYR cc_start: 0.6041 (t80) cc_final: 0.5598 (t80) REVERT: H 34 TRP cc_start: 0.8682 (m-10) cc_final: 0.8213 (m-10) REVERT: I 657 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8260 (tm-30) REVERT: J 100 LYS cc_start: 0.8969 (mmmt) cc_final: 0.8527 (tmtt) REVERT: L 77 ARG cc_start: 0.8979 (tmt170) cc_final: 0.8515 (tmt170) REVERT: L 91 PHE cc_start: 0.7863 (p90) cc_final: 0.6779 (p90) REVERT: L 98 PHE cc_start: 0.5418 (OUTLIER) cc_final: 0.3958 (t80) REVERT: N 76 ASP cc_start: 0.8538 (m-30) cc_final: 0.8319 (t70) REVERT: O 33 TYR cc_start: 0.6009 (t80) cc_final: 0.5655 (t80) REVERT: O 34 TRP cc_start: 0.8637 (m-10) cc_final: 0.8049 (m-90) REVERT: O 86 ASP cc_start: 0.0995 (p0) cc_final: 0.0713 (p0) REVERT: P 27 GLN cc_start: 0.8494 (tp-100) cc_final: 0.8127 (tp-100) REVERT: R 530 MET cc_start: 0.8705 (mmm) cc_final: 0.8448 (mmt) REVERT: R 657 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8169 (tm-30) REVERT: S 16 GLU cc_start: 0.7646 (pt0) cc_final: 0.7132 (mp0) REVERT: U 32 MET cc_start: 0.7960 (tpp) cc_final: 0.7658 (ttt) REVERT: W 1 GLN cc_start: 0.3732 (OUTLIER) cc_final: 0.2736 (pm20) REVERT: W 31 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8320 (ptp90) REVERT: W 86 ASP cc_start: 0.0543 (p0) cc_final: 0.0171 (p0) REVERT: X 13 VAL cc_start: 0.6413 (OUTLIER) cc_final: 0.6181 (t) outliers start: 75 outliers final: 58 residues processed: 275 average time/residue: 0.4416 time to fit residues: 196.0308 Evaluate side-chains 267 residues out of total 3354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 203 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 273 ARG Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain F residue 56 SER Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 119 CYS Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 288 PHE Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 491 ILE Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 89 MET Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain P residue 89 MET Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 135 THR Chi-restraints excluded: chain Q residue 202 THR Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain Q residue 424 ILE Chi-restraints excluded: chain Q residue 491 ILE Chi-restraints excluded: chain R residue 539 VAL Chi-restraints excluded: chain R residue 573 ILE Chi-restraints excluded: chain V residue 109 VAL Chi-restraints excluded: chain W residue 1 GLN Chi-restraints excluded: chain W residue 2 VAL Chi-restraints excluded: chain W residue 17 THR Chi-restraints excluded: chain W residue 31 ARG Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain X residue 2 ILE Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 13 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 6.9990 chunk 238 optimal weight: 9.9990 chunk 319 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 276 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 300 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 308 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 543 ASN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 HIS ** W 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.084974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.057337 restraints weight = 110260.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059273 restraints weight = 59637.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.060493 restraints weight = 42334.662| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33309 Z= 0.252 Angle : 0.724 14.009 45288 Z= 0.343 Chirality : 0.046 0.279 5589 Planarity : 0.005 0.053 5508 Dihedral : 9.993 111.389 7920 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.47 % Allowed : 21.47 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3801 helix: 1.22 (0.29), residues: 348 sheet: -0.36 (0.14), residues: 1269 loop : -1.11 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP W 103 HIS 0.002 0.001 HIS C 35 PHE 0.016 0.001 PHE H 78 TYR 0.021 0.001 TYR P 87 ARG 0.007 0.000 ARG P 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5866.26 seconds wall clock time: 107 minutes 29.77 seconds (6449.77 seconds total)